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1 #Dan Blankenberg
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2 import sys
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3 from galaxy_utils.sequence.fastq import fastqReader
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4 from galaxy_utils.sequence.fasta import fastaWriter
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5
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6 def main():
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7 input_filename = sys.argv[1]
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8 output_filename = sys.argv[2]
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9 input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary
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10
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11 num_reads = None
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12 fastq_read = None
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13 out = fastaWriter( open( output_filename, 'wb' ) )
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14 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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15 out.write( fastq_read )
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16 out.close()
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17 if num_reads is None:
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18 print "No valid FASTQ reads could be processed."
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19 else:
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20 print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 )
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21
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22 if __name__ == "__main__": main()
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